Molecular dynamics-of-ions-in-two-forms-of-an-electroactive-polymer

1. INTERDISCIPLINARY TRANSPORT PHENOMENA
Molecular Dynamics of Ions in Two Forms
of an Electroactive Polymer
D. A. Morton-Blake and Darren Leith
School of Chemistry, Trinity College, Dublin, Ireland
Molecular dynamics (MD) are performed in all-atom simulations of two polymer species
based on polythiophene. In one case the amphiphilic polymer forms a monolayer inter-
face between a vacuum and an aqueous layer containing ions. The electroactive nature
of the polymer is invoked by conferring a negative charge on it to compensate for charge
imbalance in the Na+
and Cl−
concentrations of the aqueous layer. The effects of hydro-
static pressure and charge imbalance on the stability of the monolayer are investigated.
In another simulation a polythiophene oligomer is wound into a helix where it serves
as an ion channel between two aqueous regions on both sides of a phospholipid bilayer
membrane.
Key words: molecular dynamics; electroactive polymer; charged monolayer; helical ion
channel
Introduction
Polythiophene chains can minimize their
steric repulsion in one of two ways. The most
common one is the anti conformation1
in which
successive sulfur atoms along the chain point
“up” and “down,” as shown in Figure 1.
The same polymer in a helical conformation
is shown in Figure 2. It is generated by twisting
the entire chain to the right of each inter-ring
bond in turn, by the same torsional angle.
The backbones of these polymers are π con-
jugated, and because this property confers on
them a reduced band gap compared with all-σ
systems, they can undergo redox changes that
permit them to acquire overall positive or neg-
ative charge, which is located principally in the
thiophene rings.
The properties of this kind of polymer are
also influenced by substituting the H atoms
on the “3” position of the thiophene rings by
various groups; alkyl substitution renders the
polymer soluble in largely nonpolar solvents,
Address for correspondence: D. A. Morton-Blake, School of Chemistry,
Trinity College, Dublin 2, Ireland. Voice: 353 1 8961943; fax: 353 1
671826. tblake@tcd.ie
whereas oxygen-containing substituents would
favor a protic environment. These properties
will be exploited in the molecular dynamics
(MD) investigations described here.
Part 1: Amphiphilic Polymer
Monolayer
Consider the substitution of the “3” posi-
tions of successive thiophene rings alternately
with an alkyl side chain, which is here the hy-
drophobic group octyl (C8H17), and with the
hydrophilic chain -(CH2-O-CH2)4-CH2-OH.
Because these “3” positions alternate along the
backbone, the side groups that they bear also al-
ternate “up” and “down,” as shown in Figure 3.
The result2
is an amphiphilic polymer with the
ability to form monolayers on a water surface;
the hydrophilic oxanoyl chains enter the aque-
ous layer, whereas the hydrophobic alkyl chains
are directed almost normal to the water sur-
face into the vacuum. We previously3
applied
MD to simulate a stable, ordered film of a self-
assembled stable monolayer interface of these
polymers at a water surface.
In a quest for materials for novel nanoscale
devices, we wish to characterize the stability of
Interdisciplinary Transport Phenomena: Ann. N.Y. Acad. Sci. 1161: 105–116 (2009).
doi: 10.1111/j.1749-6632.2009.04095.x C⃝ 2009 New York Academy of Sciences.
105

2. 106 Annals of the New York Academy of Sciences
Figure 1. An anti sequence of a polythiophene chain backbone.
Figure 2. Polythiophene in a syn conformation,
resulting in a helical chain. (In color in Annals online.)
the monolayer film to the application of hy-
drostatic pressure and when the electroactive
character of the polythiophene backbone is ex-
ploited by allowing it to assume an overall elec-
tric charge. (The charge will be compensated
by unbalancing concentrations of the Na+
and
Cl−
solutes in the water layer.)
Computation
The code used for the MD was DL_POLY,4
which was run with periodic boundary condi-
tions (forming Ewald coulombic sums along the
membrane surface) usually for 105
time steps (1
time step = 0.001 ps) in a Hoover thermostat
at 300 K at a series of constant pressures. Us-
Figure 3. The amphiphilic polymer poly(3-octyl
3′
-oxanoyl bithiophene). The red and yellow atoms
are, respectively, oxygen and sulfur. (In color in
Annals online.)
ing code written for parallel processors, such
an MD run took 90 h of CPU time on a com-
puter cluster of two nodes, both consisting of
two processors. The atomistic potentials used
were intramolecular (bond and bond angle) and
nonbonding (intermolecular), which were as-
signed according to the DREIDING generic
formulation5
—except for those involving the
water molecule, for which the SPC potentials
of Berendsen et al. were used,6
and those for
the Na+
and Cl−
ions, which were described

3. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 107
by the potentials of Rasaiah et al.7
The potential
parameters for the interactions between water
and the other atoms, and between the ions and
other atoms, were obtained by the commonly
used geometric-mean rule. Torsional potentials
in the polythiophene main chain were assigned
as described in our previous work.8
The partial atomic charges on the thiophene
rings were taken from DFT calculations on neu-
tral and charged oligothiophenes,9
and those
of the oxidized polymer main chain were as-
signed by distributing the additional charge
evenly over the five atoms of each thiophene
ring in the polymer chains. The atoms of the
hydrophobic octyl side chains were assumed
to have no net charges, and those on the
hydrophilic oxanoyl chains were taken from
the work of Udier-Blagovi´c et al.10
on model
compounds.
Monolayer Molecular Model
The unit cell constituting the MD simulation
box contained chains of poly(3-octyl 3′
-oxanoyl
bithiophene), whose primary structure was de-
scribed in the introduction and a fragment of
which is illustrated in Figure 3. The structural
repeat unit of the cell’s polymer component
consisted of two such chains with a mutual
displacement of half a bithiophene unit along
the polymer backbone. In this way steric en-
ergy was minimized because the side groups
of each chain corresponded with the gaps be-
tween those of the adjacent one when viewed
in the sense of Figure 3. The MD simulation
box was a two-dimensional unit cell in the ab
plane, consisting of six pairs of chains. The box
therefore contained a total of 12 chains along
the b axis, and 6 substituted bithiophenes along
a, making a total of 72 bithiophene units. The
polymer constituted the interface between the
vacuum and an aqueous layer, which was po-
sitioned to overlay the oxanoyl side chains. It
consisted usually of 2222 water molecules and
a total of about 290 ions from the NaCl elec-
trolyte, resulting in a 11% NaCl solution.
Results of Monolayer Investigation
Pressure
We have shown that application of lateral
pressure, which is equivalent to compressing
the monolayer by a piston in the interfacial
plane, as in a Langmuir trough, first disor-
ders and then ruptures the monolayer with in-
creasing pressure.3
Hydrostatic pressure, on the
other hand, which we describe here, is applied
isotropically to the complete system.
Electrolyte Solutions
An optimum statistical analysis of the be-
havior of the ions in the NaCl solution would
require many ions to be present in the aqueous
layer. We therefore worked with a mole fraction
of 11% NaCl in water, which is the maximum
concentration achievable under normal con-
ditions. Using the electroactive facility of the
polymer to acquire an overall electric charge
(although the electrochemical species that pro-
mote this charge were not explicitly included in
the simulation), we compensated the polymer
charge by removing the equality of the concen-
trations of the Na+
and Cl−
ions in the aque-
ous layer. We must also decide on the range of
charges to confer on the polymer and the com-
pensating electrolyte solutions. An upper limit
of such a range would normally be the max-
imum charge that oxidized electroactive poly-
mer can acquire by the transfer of electronic
charge by a redox mechanism. For heteroaro-
matic ring polymers this value is that of a chain
in which approximately half the rings acquire
a unit electron charge.11
Because there are 144
thiophene rings in our MD box and only about
145 ions in all, compensating such a large poly-
mer charge by unbalancing the concentrations
of the Na+
and Cl−
ions would be unrealistic.
Because in any case such a charge would de-
stroy the monolayer, we must use much lower
degrees of polymer oxidation or reduction. To
examine the effect on the monolayer, we there-
fore performed a series of calculations in which

4. 108 Annals of the New York Academy of Sciences
Figure 4. View of the polymer monolayer on the aqueous layer along a direction parallel to the interface,
which is also the direction of the polythiophene chains. The sulfur atoms (yellow) of the thiophene rings trace
the polymer backbone. (In color in Annals online.)
the Na+
and Cl−
ion concentrations were un-
balanced up to a maximum of 30%.
Results
Hydrostatic Pressure
Figure 4 shows the monolayer system on
an 11% aqueous NaCl solution after dynam-
ics periods of 100 ps at hydrostatic pressures
of from atmospheric to 1000 bar. In these
atomic plots the system is viewed along the
interface parallel to the directions of the poly-
mer chains. The thiophene rings in the polymer
backbone can be identified by the yellow sulfur
atoms. During the 100-ps period at 1-bar pres-
sure, order is retained in the main chains of
the polymer (though not in the side chains).
The packing of the polymers had been de-
fined in the initial (input) structure with ad-
jacent chains displaced by half a bithiophene
unit in accordance with the structures of bulk
lattice poly(alkylthiophene)s12
; in this way thio-
phene rings in adjacent chains formed a stag-
gered stacked relationship. A detailed exami-
nation of the postdynamics equilibrium struc-
tures at 1-bar pressure, however, showed that
the chains had been displaced into positions in
which the thiophene rings now showed near-
eclipsed stacking. Energy was reduced by a slight
up–down slipping of alternate chains along the
c axis (normal to the interface).
Water molecules and Na+
and Cl−
ions ap-
pear in the space of the oxanoyl side chains but
do not venture into the region occupied by the
polymer backbone. At a pressure of 10 bars sev-
eral polymer chains are displaced significantly
“upward” (into the vacuum layer) or “down-
ward” (into the aqueous layer) from their for-
mer surface positions. Because the monolayer
“seal” is broken, water molecules and the ions
can seep into the region that was formerly as-
sociated with the interface.
Because the pressures were imposed instan-
taneously at the outset of the dynamics rather
than successively, the higher pressures of 100
and 1000 bars preclude the “slipping” of the
polymer chains out of the interface region in
the manner that occurs at 10 bars. As a result,
although individual thiophene rings twist out of
their former planes normal to the interface, the
high pressures immobilize the chains in the in-
terface, sealing the region of the polymer back-
bone from invasion by water molecules and
ions, which can reach only the region of the
oxanoyl chains.
The radial distribution function (RDF) plots
in Figure 5 indicate the probabilities of finding
a specified pair of atom types at various sepa-
rations. Because one sulfur atom is present in
each thiophene ring in the polymer main chain,
the function gSS(r) in part A of the figure can
demonstrate the degree to which adjacent thio-
phene rings twist around their interconnecting

5. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 109
Figure 5. RDFs for the atom pairs (A) S . . . S and (B) S . . . O (where O is an oxygen atom in water) at
four values of hydrostatic pressure. (In color in Annals online.)
bonds. In a polythiophene chain in which the
thiophene rings are coplanar and adjacent rings
are in an anti conformation (i.e., trans in the
S−C−C−S link) the smallest S . . . S separa-
tion is that between S atoms in adjoining rings,
which is 4.31 A˚ . At a pressure of 1 bar Figure 5A
shows that the sharpest peak is a narrow one
at r = 4.18 A˚ , indicating a twist from trans
of about 45◦
around inter-ring bonds, which
would bring the S atoms closer. The peak height
increases with the application of greater pres-
sure, the maximum shifting to r = 4.3 A˚ , imply-
ing that the pressure induces greater uniformity
on the main-chain torsions. An examination of
individual chains showed that the torsional an-
gles of successive thiophene rings alternated in
a rather regular manner. From the foregoing we
can infer a result that was not obvious from the
atomic plots in Figure 2, namely, that although
hydrostatic pressure reduces the positional order
of the polymer chains their conformational order
is increased by the pressure.
In a regular planar polythiophene chain the
separation of S atoms in next-nearest-neighbor
rings is 7.76 A˚ . The second narrow g(r) peak in
Figure 5A is at r = 7.7 A˚ , a distance that does
not change significantly with pressure. How-
ever, 7.7 A˚ is also the separation of S atoms in
the near-eclipsed stacked columns of thiophene
rings, and the broader RDF peaks in this region
arise from the buckling of the main-chain di-
rections, which widens the range of separation
of the S atoms in pairs of adjacent chains.
Figure 6. The distribution of torsional angles
S−C−C−S around the inter–thiophene ring C−C
bonds in the amphiphilic polymer at the hydrostatic
pressures shown (anti, 180◦
; syn, 0◦
). The links are
in largely gauche conformations, but there is a sub-
stantial trans population (±180◦
) particularly at high
pressures.
The principal g(r) peak for the atom pair S . . .
O in Figure 5B, where O is the oxygen atom in
the water molecules, decreases markedly with
increasing applied pressure, showing that be-
cause of the denser packing of the alkanoyl side
chains at high pressures, water molecules are
denied access to the polymer backbone of the
solvent.
Figure 6 shows the distribution of torsional
angles ϕ in the polythiophene backbone. The
traces confirm our preceding conclusions
from the atom plots and the RDF curves,
that although the anti conformation of the
bithiophene unit (trans S−C−C−S, ϕ = 180◦
)
is common, most of them are in equally

6. 110 Annals of the New York Academy of Sciences
Figure 7. The surface of an 11% NaCl aqueous solution in which the monolayer bears a series of
negative charges compensated by appropriate values of excess Na+
in the electrolyte. (In color in Annals
online.)
weighted gauche conformations g+ and g− with
ϕ ≈ ±120◦
.
Charged Polymer
We have already described that redox pro-
cesses can confer overall charges on such poly-
mers as polythiophene to the extent of imposing
a unit charge (on average) on every two thio-
phene rings along the chain. However, that con-
dition would be for a bulk electrolytic medium
in which the coulombic energy is lowered by the
close approach of counterions to the charged
chain sites. We have yet to see whether the
Na+
or Cl−
ions could penetrate the region
of densely packed oxanoyl chains of the mono-
layer sufficiently readily to access the oppositely
charged thiophene rings.
A series of monolayers were simulated in
which the charge balance of the 290-ion
Na+
/Cl−
ion system in the aqueous layer (con-
stituting an 11% NaCl solution) was gradually
decoupled by converting the requisite num-
ber of Cl−
ions into Na+
ions. Distribution
of the compensating negative charge evenly on
the thiophene rings produced charged polymer
monolayers on NaCl solutions that had excess
negative charge varying from 1% to 30% of the
total ion concentration.
Figure 7 shows the structure at the water–
polymer interface after 50,000 time steps (50 ps)
for a series of systems with the charge excess
percentage in the aqueous layer indicated. The
figures show that the monolayer structure is
well preserved up to 14% excess but that it de-
teriorates markedly at higher polymer charge.
An examination of the interface region shows

7. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 111
Figure 8. RDF traces for atom pairs (A) S, O (where O is a water oxygen atom) and (B) S, Na+
in systems
of different excess charges. (In color in Annals online.)
that at 6% excess charge Na+
ions are attracted
into the interface region and begin to occupy
sites between the polymer’s stacked (negatively
charged) thiophene rings. The fact that no
uncharged water molecules make it into this re-
gion for the neutral polymer (at least in the time
scale of the MD) and that it is observed to occur
only when there is an Na+
/Cl−
charge imbal-
ance in the aqueous layer demonstrates the ef-
fectiveness of the electric field arising from the
coulombic charge on the polymer main chain
in attracting the Na+
ions and water molecules
of hydration.
Because of the short intervals characterizing
MD runs, it is difficult to specify the critical
charge excess that ruptures the monolayer. In-
terfaces that have achieved stability after 105
time steps (0.1 ns) might be found to destabi-
lize in laboratory intervals that are inaccessible
to MD. But it is apparent from the results pre-
sented here that a polymer monolayer with no
overall charge is more stable than a charged
monolayer. Investigations have been cited of
electroactive polymer films that have been sub-
jected to a maximum oxidation that confers a
unit charge on every three rings.13
A mono-
layer instability setting in (as suggested by our
results, say) 10% charge excess implies an ex-
cess of 30 Na+
in 290 ions. This requires that
the compensating charge of −30e is distributed
over the 144 thiophene rings of the polymer.
On average, then, one unit negative charge
would be distributed over about five thiophene
rings. This might well be possible in a polymer
film or poly(3-alkylthiophene) solution, where
we have shown9
that counterions can access
the charged rings and lower the electrostatic
energy by forming ion pairs with the oppo-
sitely charged site on the polymer. However,
in a system such as the one considered here
the acquisition of one charge per three rings
would correspond to 48 charges spread over
144 thiophene rings and a charge imbalance of
16.5% between the polymer and the 290 ions in
solution.
Because the monolayer starts to break down
at 11% charge excess, such an imbalance would
be fatal to the structure of the monolayer. We
have mentioned the entry of Na+
ions and a
few H2O molecules of hydration into the inter-
face region for monomer/aqueous-electrolyte
systems shown in Figure 7 with the Na+
con-
centration exceeding that of the Cl−
ions. More
details of this event are presented in Figure 8,
which shows the RDF functions between the
S atoms of the thiophene ring and the Na+
ions in part A of the figure and between S
and the water oxygen atoms in part B. Al-
though the penetration of both species into
the interface region occurs, a comparison of
the amplitude of the g(r) scale between parts
A and B of the figure confirms the results
from the atom plots, that the electric field of
the charged polymer attracts the Na+
ions
more strongly than the water atoms, the lat-
ter probably arriving in the interface through
participation in the solvent sheaths of the
Na+
ions.

8. 112 Annals of the New York Academy of Sciences
Figure 9. Phospholipid dipalmitoyl-phosphatidyl
choline (DPPC).
Part 2: Amphiphilic Polymer Ion
Channel
Molecular Model
The transport of ions across a cellular mem-
brane is central to the functioning of a liv-
ing cell. Recognizing the advances being made
in nanoscience, we consider the possibility of
a synthetic channel that conducts ions across
a conventional bilayer membrane consisting
of the amphiphilic phospholipid zwitterion di-
palmitoyl phosphatidyl choline (DPPC), whose
molecular structure is shown in Figure 9. The
polar head group consists of a trimethylammo-
nium cation, a negatively charged phosphate
anion, and two hydrophobic C14 alkyl chain
tails. The artificial transporter is a short length
of a polythiophene derivative that is twisted into
a helical conformation. The resulting rather
rigid channel possesses the electroactive prop-
erty of being capable of maintaining a charge of
either sign. The DPPC phospholipid molecules
were assembled with their alkyl chains perpen-
dicular to a two-dimensional ab plane, defining
a structural cell with periodic boundary con-
ditions in the plane of the membrane. A “ba-
sic” cell contained two DPPC molecules, whose
relative orientations were varied to minimize
packing forces, which occurred when the car-
bon planes of the (four) alkyl chains were almost
parallel. The structural cell was then assembled
into a 4 × 6 supercell, which contained a to-
tal of 96 phospholipid molecules placed end to
end to form a bilayer, leaving a gap of 0.75
A˚ between the closest hydrogen atoms in the
terminal methyl groups in the two monolay-
ers. The two aqueous layers, each of depth
32.3 A˚ , consisting of 4000 water molecules di-
vided equally between the layers, were sepa-
rated by two lengths of phospholipid chain,
each 17.93 A˚ . If we include the tip-to-tip gap
between the alkyl chains, the aqueous regions
were thus separated by distance of 36.5 A˚ . Na+
and Cl−
ions were then created in the aque-
ous layers by replacing water molecules with
ions at regular separations that were consistent
with the required NaCl concentrations, which
were around 0.015 M. Ionic imbalances could
be created by varying the relative sodium and
chloride concentrations in such a way that the
n(Na+
):n(Cl−
) ratio in one layer was precisely
matched by its inverse n(Cl−
):n(Na+
) ratio in
the other to preserve overall charge neutrality.
Ion Transporter Channel
We simulated a substitutional derivative of
an oligothiophene chain, which in Figure 10
is shown in the planar all-anti conformation.
When the entire chain to the right of the inter-
ring bond labeled a is twisted by 175◦
about a,
and the process repeated in turn around each
inter-ring bond to the right along the chain, a
tight helical conformation is generated. The ex-
ternal and internal diameters of the helix are,
respectively, 21.0 and 11.5 A˚ , and the screw
axes have close to 11 thiophene rings per turn.
Such helices of polythiophene and polypyrrole
have been observed in the solid phase and in
solution and have been structurally character-
ized.14
For the helical chain to function as an
ion channel it must span the 35.9-A˚ thickness
of the membrane between the two aqueous lay-
ers. For this purpose an oligothiophene chain
consisting of 94 thiophene rings was simulated.
Also, the chain must be capable of hydrophilic
association with the aqueous layers above and
below the phospholipid membrane as well as
lipophilic association with the membrane bi-
layer itself. For this reason hydrogen atoms in
the thiophene “3” positions on the 11 rings at
each end of the chain are substituted by polar

9. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 113
Figure 10. The terminal portion of the substituted oligothiophene chain showing the polar
(left) and nonpolar (right) rings.
Figure 11. The 94-ring oligothiophene helix ion channel, lateral and axial views (A) and (B). The black,
white, yellow, and red atoms are, respectively, those of carbon, hydrogen, oxygen, and sulfur. (In color in
Annals online.)
hydroxyl groups, and each terminal ring in ad-
dition is “capped” with a carboxylic acid group,
COOH. In this way the “first” and “last” com-
plete turn in the helix, both of which contacted
the aqueous electrolyte layers, were rendered
hydrophilic. The remaining 72 rings of the he-
lix, which were embedded in the membrane’s
nonpolar phospholipid tails, were made hy-
drophobic by substituting in the “3” positions
with methyl groups. The resulting chain is illus-
trated in Figure 11, where the atoms are iden-
tified by the colors in the figure caption and
Figure 12 shows the predynamics extent of the
helix channel bridging the aqueous layers on
both sides of the DPPC membrane. The single
turn of the coil in each layer has been rendered
hydrophilic by the substitution of hydroxyl and
carboxylic groups, whereas the remaining coils,

10. 114 Annals of the New York Academy of Sciences
Figure 12. The polythiophene helix of Figure 11
embedded in a DPPC bilayer and two layers of aque-
ous NaCl solution prior to the MD; (A) side and (B)
axial view. (In color in Annals online.)
which are embedded in the bilayer membrane,
are made hydrophobic by methyl groups.
The bridged membrane structure, relaxed
by the MD, is shown in Figure 13. In part B,
the phospholipid molecules have been removed
to show the helix, which is still anchored to
the aqueous layers and to the membrane by
its hydrophilic and hydrophobic moieties. Al-
though the chain exhibits distortions compared
to Figure 11, their dynamic nature retains a
channel whose diameter averages 6–7 A˚ .
Because the aim is to study the migration of
ions along the transporter channel, we placed
the ions in the two aqueous layers near each
end of the helix channel bridging the layers
to avoid prohibitively long MD run times. Al-
though charge neutrality was preserved by cre-
ating equal numbers of Na+
and Cl−
ions over-
all, a charge imbalance between the aqueous
layers was sometimes created by allowing the
composition of the ion mixture to vary at each
end of the channel.
DPPC molecules have been removed to ex-
pose the oligothiophene helix bridging the two
layers. The helix channel is revealed by the yel-
low sulfur atoms in the thiophene rings. Blue
and green atoms show Na+
and Cl−
ions, re-
spectively, in the aqueous layers.
The migration of the ions was monitored
by RDF functions for which the atom pairs
selected were (Na+
, S) and (Cl−
, S) for, as is
clear from Figure 11, sulfur is a unique atom
species to the interior of the channel. By 105
time steps (100 ps) the ions in the channel have
reached a steady-state concentration and the
rather scattered (because of the paucity of Na+
and Cl−
ions) RDF traces in Figure 14 show the
progress of the three migrating species—Na+
,
Cl−
, and the water molecules—along the chan-
nel. Not surprisingly, because the thiophene
S atom bears partial charges of +0.26e, the
strongest peaks are those for the Cl−
ions, which
show temporary halting sites (or slowdown re-
gions) at roughly evenly spaced intervals of 3.6,
5.2, 7.2, 8.4, and 10.2 A˚ , whereas those for the
Na+
ion are less well defined with a principal
Na+
–S distance of 6 A˚ . The water molecules,
although polar, do not show well-defined asso-
ciations with the channel atoms.
Conclusions
The two structural modifications of polythio-
phene described in this work demonstrate the
wide properties of this electroactive polymer.
We have shown that the amphiphilic properties
of both 3-octyl 3′
-oxanoyl and the derivatized
helical 3-methyl polythiophene species can
be deployed to perform nanoscale activities,

11. Morton-Blake & Leith: Molecular Dynamics of Ions in a Polymer 115
Figure 13. (A) The phospholipid bilayer membrane separates the two aqueous layers
(red O atoms). In (B) DPPC molecules have been removed to expose the oligothiophene
helix bridging the two layers. The helix channel is revealed by the yellow sulfur atoms in the
thiophene rings. Blue and green atoms show Na+
and Cl−
ions, respectively, in the aqueous
layers. (In color in Annals online.)
provided that the excess charge is less than
about 12%. However, the stabilizing effect of
hydrostatic pressure provides hope that even
a charged monolayer film may be preserved.
The charged monolayer formed by the alkyl–
oxanoyl polymer opens up the possibility that
the material might be used in multilayers as
a molecular membrane separating protic and
nonprotic liquid layers such as water and chlo-
roform, which we are currently investigating.
The polymer’s ability to occlude ions from the
layers could confer novel properties on the re-
sulting mono- and multilayer systems.
To our knowledge, the use of the helical poly-
mer to form an ion transporter between two
nanoscale aqueous electrolyte regions as de-
scribed in the second part of the work has not
hitherto been proposed, but a simple channel
Figure 14. RDF traces expressing the associa-
tions of the three migrating species along the poly-
thiophene helix channel. (In color in Annals online.)
of this kind might be a valuable for practical in-
vestigations into the migration of ions, solvent
molecules, and other dissolved species bridging
electrolyte systems.

12. 116 Annals of the New York Academy of Sciences
Acknowledgment
We acknowledge support from Instit´ud um
Theicneola´ıcht Eolais agus Riomhfhorbairt
(IITAC).
Conflicts of Interest
The authors declare no conflicts of interest.
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